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- PDB-5chf: Crystal structure of murine ISG15 in space group P21212 -

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Basic information

Entry
Database: PDB / ID: 5chf
TitleCrystal structure of murine ISG15 in space group P21212
ComponentsUbiquitin-like protein ISG15
KeywordsANTIVIRAL PROTEIN / ubiquitin-like protein / cell cycle
Function / homology
Function and homology information


positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication ...positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / polyubiquitin modification-dependent protein binding / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / response to bacterium / response to virus / modification-dependent protein catabolic process / protein tag activity / positive regulation of type II interferon production / integrin binding / ubiquitin-dependent protein catabolic process / defense response to virus / defense response to bacterium / ubiquitin protein ligase binding / extracellular region / cytosol
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsFritz, G. / Basters, A.
CitationJournal: To Be Published
Title: Crystal structure of murine ISG15 in space group P21212
Authors: Fritz, G. / Basters, A.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein ISG15
B: Ubiquitin-like protein ISG15
C: Ubiquitin-like protein ISG15
D: Ubiquitin-like protein ISG15
E: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,51712
Polymers86,8605
Non-polymers6577
Water2,882160
1
A: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7445
Polymers17,3721
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3721
Polymers17,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3721
Polymers17,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6564
Polymers17,3721
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)17,3721
Polymers17,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 168.290, 85.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-202-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALALEULEUchain AAA2 - 1502 - 150
2ALAALAARGARGchain BBB2 - 1512 - 151
3ALAALALEULEUchain CCC2 - 1502 - 150
4TRPTRPARGARGchain DDD3 - 1513 - 151
5ALAALAARGARGchain EEE2 - 1512 - 151

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Components

#1: Protein
Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein


Mass: 17372.021 Da / Num. of mol.: 5 / Mutation: C76S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isg15, G1p2, Ucrp / Plasmid: pTXB1 / Details (production host): intein fusion / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64339
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.7 M (NH4)2 SO4, 0.06 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37611 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 41 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.197 / Χ2: 1.014 / Net I/σ(I): 10.91 / Num. measured all: 267134
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.46.50.5471.7621.0428105448443141.91996.2
2.4-2.60.7711.1941.8151434700469911.28599.8
2.6-2.80.8610.8012.8738071517051670.86299.9
2.8-30.9390.5174.8528415390638920.55799.6
3-40.990.19513.0469382989197780.21198.9
4-60.9980.06729.1236195519551650.07299.4
6-80.9980.05430.699115130413030.05899.9
80.9990.0341.546417102310010.03397.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z2M

1z2m


Resolution: 2.3→47.966 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 1832 4.87 %
Rwork0.2077 35749 -
obs0.2105 37581 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.76 Å2 / Biso mean: 63.9241 Å2 / Biso min: 22.48 Å2
Refinement stepCycle: final / Resolution: 2.3→47.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5883 0 39 160 6082
Biso mean--67.8 55.57 -
Num. residues----747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066010
X-RAY DIFFRACTIONf_angle_d1.0788108
X-RAY DIFFRACTIONf_chiral_restr0.049942
X-RAY DIFFRACTIONf_plane_restr0.0061025
X-RAY DIFFRACTIONf_dihedral_angle_d14.7512265
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3629X-RAY DIFFRACTION14.533TORSIONAL
12B3629X-RAY DIFFRACTION14.533TORSIONAL
13C3629X-RAY DIFFRACTION14.533TORSIONAL
14D3629X-RAY DIFFRACTION14.533TORSIONAL
15E3629X-RAY DIFFRACTION14.533TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.36220.4051410.33552568270995
2.3622-2.43180.40551290.32292721285098
2.4318-2.51020.33261450.287727182863100
2.5102-2.60.35461340.268527262860100
2.6-2.7040.34161350.266227372872100
2.704-2.82710.31141450.253527412886100
2.8271-2.97610.30171510.232627342885100
2.9761-3.16260.29951500.21382736288699
3.1626-3.40670.27431340.19612776291099
3.4067-3.74940.25421510.18682716286799
3.7494-4.29160.20061480.15492754290298
4.2916-5.40580.19121340.158728472981100
5.4058-47.97640.27781350.22052975311099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.7044-5.20170.82938.5966-2.94151.8402-0.50711.1138-1.0557-0.96760.55661.26891.6712-0.620.14421.3725-0.32050.15950.8634-0.02020.4967-11.49214.3816-51.3293
24.065-1.6598-0.71547.8915-2.24248.1469-0.84970.418-1.1436-1.09771.06810.61331.3193-1.04390.2250.9589-0.31030.10590.73250.07140.51-9.2365.6939-49.5693
35.16491.4515-1.35071.8543-1.98112.7555-0.8570.0309-0.9008-0.9032-0.5044-1.51671.55760.97860.87310.67020.10080.23430.34510.05970.4963-3.6769.456-47.2182
43.00021.4259-2.05897.4569-3.42457.5393-0.47580.2959-0.1998-0.28110.16410.48470.8642-0.93610.39380.2805-0.04770.03960.3895-0.0410.3938-10.954111.6061-40.9557
53.33940.3614-0.98344.91021.22045.8697-0.203-0.0029-0.0994-0.1301-0.1404-0.04790.5151-0.03690.1380.3141-0.01550.15860.33120.04180.2426-5.021714.826-36.1698
62.6040.753-0.7445.20172.16646.7012-0.0475-0.01620.16420.00810.2173-0.3708-0.56591.1854-0.20810.2865-0.04130.10110.4092-0.06580.41461.878429.9458-31.0552
73.61763.3896-0.61319.1223-1.16135.48740.7375-0.14210.69360.5777-0.0505-0.5999-0.99691.318-0.31010.4834-0.12770.20310.9314-0.08620.646711.861532.7091-30.6777
86.1748-1.69862.18265.0865-1.04746.21260.1904-0.96390.3934-0.19670.6174-1.0438-0.36631.0482-0.14390.51840.03310.25650.6419-0.09120.50948.878324.8318-40.3139
92.81710.433-0.38213.7129-2.24165.0483-0.0295-0.60840.2365-0.2377-0.1366-0.57070.9151.4265-0.34230.22230.04680.07650.6815-0.01740.47926.643821.5179-32.8415
104.4144-1.4863-0.13356.50780.84332.6523-0.2877-0.17370.15790.53170.2049-0.06020.1242-0.07880.08980.4827-0.03570.0580.3092-0.05970.2594-9.317439.2555-20.0095
114.46134.65830.76084.75260.08960.20.55490.1661-0.01111.8177-0.34640.23110.01320.3217-0.09040.79870.03630.07380.4155-0.00390.3556-11.36124.4479-16.052
126.03770.732-1.9824.8153-1.08396.3828-0.53150.2839-1.00440.25650.10830.43790.346-0.79190.160.43420.02430.16180.3666-0.12760.4573-18.420510.4864-19.4259
133.12981.1309-1.25154.64680.07375.7106-0.37710.0581-0.6691-0.16360.1128-0.10150.7108-0.16210.27810.3985-0.00490.11590.2935-0.0260.3963-13.62829.3802-25.0683
144.229-2.58481.78514.3321-0.22379.55940.0478-0.2089-0.33950.0756-0.0212-0.0718-0.00440.5765-0.01170.40540.01420.16740.38880.08680.469-14.6933.8616-4.2852
153.05580.68320.69965.14480.71622.83070.0148-0.6568-0.80270.6875-0.03160.0267-0.18-0.3540.10.70960.00240.11160.6330.12730.5939-20.34052.10371.9442
163.27250.20470.3362.56651.27884.36010.642-0.19590.81631.116-0.20750.2774-1.40320.4312-0.60170.8393-0.14380.23620.4558-0.08190.5533-27.689433.73231.4084
173.80880.4351-1.63736.1311-1.56613.0680.70130.34430.4565-0.0314-0.310.1371-1.0844-0.0446-0.31380.6610.04280.22690.4730.01930.3687-27.195129.4259-7.0788
186.4786-5.56650.38114.7756-0.21661.50110.1851-0.53210.0427-0.2934-0.00381.2877-1.8549-0.8089-0.49831.24490.39580.20110.56460.2670.7905-51.405230.8321-5.8128
197.4573-3.5461.47151.89230.65818.0030.19281.2419-1.18110.42530.55770.5368-1.8521-0.0107-0.45231.15970.19720.2530.68910.21760.8614-49.982527.9288-4.487
207.2003-2.2634-0.87063.6911-0.80848.68490.83130.3405-0.13580.63780.75992.25240.3202-0.4465-0.52860.44480.21810.15450.53740.18650.8045-44.795923.5289-1.489
218.3835-2.12940.78832.46462.01235.51930.5457-1.14830.58780.4543-0.071.099-0.1727-1.0906-0.45910.59060.15230.34620.64650.18520.9501-49.314528.0885.882
221.9099-0.97082.13761.9206-2.38325.04241.1967-0.570.3190.21270.2270.6244-1.0906-2.1007-0.41950.92910.36680.22751.01290.37320.6848-50.292430.30044.5641
236.9652-3.71240.77763.6919-1.41516.4661-0.8865-0.192-1.42620.51010.33630.25490.53580.09360.45490.43760.05220.25090.38080.06910.5397-36.007911.200123.1085
244.9795-1.96240.43975.60440.06514.7435-0.2681-0.0433-0.16680.33120.1511-0.65430.14150.47410.01720.34440.02820.15050.2828-0.04420.3516-27.049915.333319.3928
252.7407-0.63030.63291.86710.43315.62030.51030.2271-0.4691-0.4985-0.3286-0.31990.36620.87190.07080.4726-0.01710.15260.4779-0.14610.4593-29.878915.14288.6267
262.8773-3.3924-0.99637.4372-0.38594.7077-0.74571.0181-0.8791-0.3160.3644-0.09950.5721-0.54820.21010.4313-0.08790.18550.2156-0.10330.4497-34.801312.613214.3946
275.1366-1.63960.944.6074-2.54266.6576-0.9803-2.33280.88470.7680.051-0.9273-1.3994-0.59150.51480.51850.221-0.13340.8787-0.13930.5791-30.022823.795835.2159
285.6310.56041.69454.53390.12513.5114-0.9847-1.35630.49140.88040.6891-1.0573-0.73870.38220.34450.98650.4308-0.24831.2117-0.19760.7344-34.024323.21742.8142
293.71141.60690.71973.67350.38466.26720.31930.76910.3383-0.3787-0.02940.6393-0.104-0.8388-0.24190.36310.06250.12580.62770.12590.437-60.828421.595726.5177
304.0869-1.9008-1.32973.4826-0.84431.86530.44570.89340.4501-0.1371-0.19790.258-0.3032-0.3453-0.22470.45720.13530.18380.54840.16310.4389-52.970426.185724.0672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 24 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 36 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 56 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 90 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 112 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 124 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 125 through 134 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 135 through 150 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 67 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 85 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 101 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 151 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 46 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 47 through 78 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 79 through 90 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 91 through 150 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 3 through 9 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 10 through 24 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 25 through 36 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 37 through 58 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 59 through 79 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 80 through 96 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 97 through 124 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 125 through 134 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 135 through 151 )D0
27X-RAY DIFFRACTION27chain 'E' and (resid 2 through 46 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 47 through 79 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 80 through 123 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 124 through 151 )E0

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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